skpkg: apply black to all files in the project directory

.flake8

@@ -6,7 +6,7 @@ exclude =
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
+    docs/source/conf.py
 max-line-length = 79
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -13,30 +13,30 @@ assignees: ""
 - [ ] License information is verified as correct. If you are unsure, please comment below.
 - [ ] Locally rendered documentation contains all appropriate pages, including API references (check no modules are
       missing), tutorials, and other human-written text is up-to-date with any changes in the code.
-- [ ] Installation instructions in the README, documentation, and the website (e.g., diffpy.org) are updated.
+- [ ] Installation instructions in the README, documentation, and the website are updated.
 - [ ] Successfully run any tutorial examples or do functional testing with the latest Python version.
 - [ ] Grammar and writing quality are checked (no typos).
 - [ ] Install `pip install build twine`, run `python -m build` and `twine check dist/*` to ensure that the package can be built and is correctly formatted for PyPI release.
 
-Please mention @sbillinge here when you are ready for PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
+Please tag the maintainer (e.g., @username) in the comment here when you are ready for the PyPI/GitHub release. Include any additional comments necessary, such as version information and details about the pre-release here:
 
 ### PyPI/GitHub full-release preparation checklist:
 
 - [ ] Create a new conda environment and install the rc from PyPI (`pip install <package-name>==??`)
 - [ ] License information on PyPI is correct.
-- [ ] Docs are deployed successfully to `https://www.diffpy.org/<package-name>`.
+- [ ] Docs are deployed successfully to `https://<github-username-or-orgname>/<package-name>`.
 - [ ] Successfully run all tests, tutorial examples or do functional testing.
 
-Please let @sbillinge know that all checks are done and the package is ready for full release.
+Please let the maintainer know that all checks are done and the package is ready for full release.
 
 ### conda-forge release preparation checklist:
 
-<!-- After @sbillinge releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
+<!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
 - [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
-- [ ] Close any open issues on the feedstock. Reach out to @bobleesj if you have questions.
-- [ ] Tag @sbillinge and @bobleesj for conda-forge release.
+- [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
+- [ ] Tag the maintainer for conda-forge release.
 
 ### Post-release checklist
 

.github/workflows/build-wheel-release-upload.yml

@@ -8,11 +8,11 @@ on:
 
 jobs:
   release:
-    uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
-      project: diffpy.labpdfproc
+      project: diffpy.my-labpdfproc
       c_extension: false
-      github_admin_username: sbillinge
+      maintainer_GITHUB_username: sbillinge
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

.github/workflows/check-news-item.yml

@@ -7,6 +7,6 @@ on:
 
 jobs:
   check-news-item:
-    uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
-      project: diffpy.labpdfproc
+      project: diffpy.my-labpdfproc

.github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -12,51 +12,10 @@ on:
 
 jobs:
   matrix-coverage:
-    defaults:
-      run:
-        shell: bash -l {0}
-
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-        python-version: ["3.11", "3.12", "3.13"]
-    env:
-      LATEST_PYTHON_VERSION: "3.13"
-    steps:
-      - name: Check out diffpy.labpdfproc
-        uses: actions/checkout@v4
-
-      - name: Initialize miniconda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: test
-          auto-update-conda: true
-          environment-file: environment.yml
-          auto-activate-base: false
-          python-version: ${{ matrix.python-version }}
-
-      - name: Conda config
-        run: >-
-          conda config --set always_yes yes
-          --set changeps1 no
-
-      - name: Install diffpy.labpdfproc and requirements
-        run: |
-          conda install --file requirements/tests.txt
-          conda install --file requirements/conda.txt
-          pip install gooey
-          python -m pip install . --no-deps
-
-      - name: Validate diffpy.labpdfproc
-        run: |
-          pytest --cov
-          coverage report -m
-          codecov
-
-      - name: Upload coverage to Codecov
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == env.LATEST_PYTHON_VERSION
-        uses: codecov/codecov-action@v4
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+    uses: scikit-package/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
+    with:
+      project: diffpy.my-labpdfproc
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/publish-docs-on-release.yml

@@ -5,8 +5,8 @@ on:
 
 jobs:
   docs:
-    uses: Billingegroup/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_publish-docs-on-release.yml@v0
     with:
-      project: diffpy.labpdfproc
+      project: diffpy.my-labpdfproc
       c_extension: false
       headless: false

.github/workflows/tests-on-pr.yml

@@ -1,53 +1,15 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
-  validate:
-    defaults:
-      run:
-        shell: bash -l {0}
-
-    runs-on: ubuntu-latest
-    steps:
-      - name: Check out diffpy.labpdfproc repository
-        uses: actions/checkout@v4
-
-      - name: Initialize miniconda
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          activate-environment: test
-          auto-update-conda: true
-          environment-file: environment.yml
-          auto-activate-base: false
-          python-version: 3.13
-
-      - name: Conda config
-        run: >-
-          conda config --set always_yes yes
-          --set changeps1 no
-
-      - name: Install diffpy.labpdfproc and requirements
-        run: |
-          conda install --file requirements/tests.txt
-          conda install --file requirements/conda.txt
-          pip install gooey
-          python -m pip install . --no-deps
-
-      - name: Validate diffpy.labpdfproc
-        run: |
-          pytest --cov
-          coverage report -m
-          codecov
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
-        with:
-          verbose: true
-          fail_ci_if_error: true
-          token: ${{ secrets.CODECOV_TOKEN }}
+  tests-on-pr:
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    with:
+      project: diffpy.my-labpdfproc
+      c_extension: false
+      headless: false
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.gitignore

@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

AUTHORS.rst

@@ -1,10 +1,10 @@
 Authors
 =======
 
-Billinge Group and community contributors.
+Sangjoon Lee, Simon Billinge, Billinge Group members
 
 Contributors
 ------------
 
 For a list of contributors, visit
-https://github.com/diffpy/diffpy.labpdfproc/graphs/contributors
+https://github.com/diffpy/diffpy.my-labpdfproc/graphs/contributors

CHANGELOG.rst

@@ -1,56 +1,5 @@
 =============
-Release Notes
+Release notes
 =============
 
 .. current developments
-
-0.2.0
-=====
-
-**Added:**
-
-* Support for Python 3.13
-
-**Removed:**
-
-* Support for Python 3.10
-
-
-0.1.3
-=====
-
-**Added:**
-
-* generate package API doc
-* redo cookiecutter to add issue templates and update readme
-
-
-0.1.2
-=====
-
-**Added:**
-
-* polynomial interpolation as the default method for cve computation.
-
-**Fixed:**
-
-* add PyPI packages under pip.txt
-
-
-
-0.1.1
-=====
-
-
-
-0.1.1
-=====
-
-
-
-0.1.0
-=====
-
-
-
-Initial release of labPDFproc.  Please see README and documentation for details

MANIFEST.in

@@ -3,7 +3,6 @@ graft tests
 graft requirements
 
 include AUTHORS.rst LICENSE*.rst README.rst
-include src/diffpy/labpdfproc/data *
 
 # Exclude all bytecode files and __pycache__ directories
 global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.